allow subworkflow name in input JSON key

To supply an optional input for a subworkflow call, Cromwell input JSON expects the key to include (i) the workflow name, (ii) the call name, (iii) the subworkflow name, and finally (iv) the input name. The need to include (iii) the subworkflow name is questionable, as discussed on openwdl/wdl#340

This change makes miniwdl accept such inputs either with or without the subworkflow name, by removing it if it's present. To ensure unambiguous resolution, also forbids collision between a call's name and that of its containing workflow.

#193

WDL/Lint.py

@@ -478,7 +478,6 @@ def call(self, obj: Tree.Call) -> Any:
 class NameCollision(Linter):
     # Name collisions between
     # - call and import
-    # - call and its containing workflow
     # - call and struct type/alias
     # - decl and import
     # - decl and workflow
@@ -503,13 +502,10 @@ def call(self, obj: Tree.Call) -> Any:
             if imp.namespace == obj.name:
                 msg = "call name '{}' collides with imported document namespace".format(obj.name)
                 self.add(obj, msg)
-        if doc.workflow and doc.workflow.name == obj.name:
-            msg = "call name '{}' collides with workflow name".format(obj.name)
-            self.add(obj, msg)
         for stb in doc.struct_typedefs:
             assert isinstance(stb, Env.Binding) and isinstance(stb.value, Tree.StructTypeDef)
             if stb.name == obj.name:
-                msg = "call name '{}' colides with {}struct type".format(
+                msg = "call name '{}' collides with {}struct type".format(
                     obj.name, "imported " if stb.value.imported else ""
                 )
                 self.add(obj, msg)

WDL/Tree.py

@@ -483,6 +483,11 @@ def resolve(self, doc: "Document") -> None:
                         self.callee = task
         if self.callee is None:
             raise Error.NoSuchTask(self, ".".join(self.callee_id))
+        assert doc.workflow
+        if self.name == doc.workflow.name:
+            raise Error.MultipleDefinitions(
+                self, "Call's name may not equal the containing workflow's"
+            )
         assert isinstance(self.callee, (Task, Workflow))
 
     def add_to_type_env(

WDL/__init__.py

@@ -178,6 +178,11 @@ def values_from_json(
             key2 = key
             if namespace and key.startswith(namespace):
                 key2 = key[len(namespace) :]
+            if key2 not in available:
+                # attempt to simplify <call>.<subworkflow>.<input>
+                key2parts = key2.split(".")
+                if len(key2parts) == 3 and key2parts[0] and key2parts[1] and key2parts[2]:
+                    key2 = ".".join([key2parts[0], key2parts[2]])
             try:
                 ty = available[key2]
             except KeyError:

test_corpi/contrived/contrived.wdl

@@ -17,7 +17,7 @@ workflow contrived {
         Float required
     }
     Int? fallaciously_optional = 123
-    call popular as contrived { input:
+    call popular as c1 { input:
         popular = popular,
         i = fortytwo,
         y = [select_first([fortytwo,23])]
@@ -28,8 +28,8 @@ workflow contrived {
     Pair[Pair[String,String],Pair[Int,Int]] p2 = ((c2.left_contents, c2.right_contents), (4,2))
 
     output {
-        Int read_int = read_json(contrived.json) + p2.right.left + p2.right.right
-        Array[Boolean] read_array = read_json(contrived.json)
+        Int read_int = read_json(c1.json) + p2.right.left + p2.right.right
+        Array[Boolean] read_array = read_json(c1.json)
         String left_contents = p2.left.left
         String right_contents = p2.left.right
     }

tests/test_2calls.py

@@ -319,6 +319,15 @@ def test_collision(self):
         with self.assertRaises(WDL.Error.MultipleDefinitions):
             doc.typecheck()
 
+        txt = task_no_outputs + r"""
+        workflow contrived {
+            call p as contrived
+        }
+        """
+        doc = WDL.parse_document(txt)
+        with self.assertRaises(WDL.Error.MultipleDefinitions):
+            doc.typecheck()
+
     def test_if_defined(self):
         # test how we typecheck a construct like
         #   if defined(x) then EXPR_WITH_x else SOME_DEFAULT
@@ -497,8 +506,8 @@ def test_io_propagation(self):
         doc.workflow.available_inputs.resolve("popular")
         doc.workflow.available_inputs.resolve("fortytwo")
         doc.workflow.available_inputs.resolve("required")
-        self.assertTrue(doc.workflow.available_inputs.has_namespace("contrived"))
-        doc.workflow.available_inputs.resolve("contrived.opt")
+        self.assertTrue(doc.workflow.available_inputs.has_namespace("c1"))
+        doc.workflow.available_inputs.resolve("c1.opt")
         self.assertTrue(doc.workflow.available_inputs.has_namespace("c2"))
         doc.workflow.available_inputs.enter_namespace("c2").resolve("opt")
         doc.workflow.available_inputs.enter_namespace("c2").resolve("i")

tests/test_3corpi.py

@@ -247,15 +247,15 @@ class dxWDL(unittest.TestCase):
 
 @wdl_corpus(
     ["test_corpi/contrived/**"],
-    expected_lint={'UnusedImport': 4, 'NameCollision': 30, 'StringCoercion': 4, 'FileCoercion': 2, 'NonemptyCoercion': 1, 'UnnecessaryQuantifier': 2, 'UnusedDeclaration': 2, "IncompleteCall": 2, 'SelectArray': 1},
+    expected_lint={'UnusedImport': 4, 'NameCollision': 27, 'StringCoercion': 4, 'FileCoercion': 2, 'NonemptyCoercion': 1, 'UnnecessaryQuantifier': 2, 'UnusedDeclaration': 2, "IncompleteCall": 2, 'SelectArray': 1},
     blacklist=["check_quant", "incomplete_call"],
 )
 class Contrived(unittest.TestCase):
     pass
 
 @wdl_corpus(
     ["test_corpi/contrived/**"],
-    expected_lint={'UnusedImport': 6, 'NameCollision': 49, 'StringCoercion': 9, 'FileCoercion': 4, 'OptionalCoercion': 3, 'NonemptyCoercion': 2, 'UnnecessaryQuantifier': 4, 'UnusedDeclaration': 9, 'IncompleteCall': 3, 'ArrayCoercion': 2, 'SelectArray': 4},
+    expected_lint={'UnusedImport': 6, 'NameCollision': 43, 'StringCoercion': 9, 'FileCoercion': 4, 'OptionalCoercion': 3, 'NonemptyCoercion': 2, 'UnnecessaryQuantifier': 4, 'UnusedDeclaration': 9, 'IncompleteCall': 3, 'ArrayCoercion': 2, 'SelectArray': 4},
     check_quant=False,
     blacklist=["incomplete_call"],
 )

tests/test_6workflowrun.py

@@ -580,6 +580,20 @@ def test_subworkflow(self):
         self.assertEqual(outputs["sums"], [1, 5, 14])
         self.assertEqual(outputs["sum"], 20)
 
+        subwf_input = R"""
+        version 1.0
+        import "sum_sq.wdl" as lib
+
+        workflow subwf_input {
+            call lib.sum_sq as summer
+            output {
+                Int ans = summer.ans
+            }
+        }
+        """
+        self._test_workflow(subwf_input, {"summer.n": 3})
+        self._test_workflow(subwf_input, {"summer.sum_sq.n": 3})
+
     def test_host_file_access(self):
         exn = self._test_workflow("""
         version 1.0